1. Field of the Invention
The present invention relates to different types of optical interrogation systems and methods capable of interrogating a two-dimensional (2D) array of optical sensors (e.g., grating coupled waveguide sensors) located for example in a multiwell plate.
2. Description of Related Art
Today there is considerable interest in developing instrumentation to enable high throughput screening (HTS) of bio-chemical interactions or binding events using optical sensors located in standardized multiwell plates. The targeted applications include drug discovery and screening, laboratory diagnosis, and fundamental research. The advantage of the standard multiwell plate format is that it allows existing automated HTS and manual fluid handling systems to be used in conjunction with novel biosensing elements. The most desirable standardized formats are 96 multiwell plates (9 mm specimen spacing), 384 multiwell plates (4.5 mm specimen spacing), and 1536 multiwell plates (2.25 mm specimen spacing). All of these multiwell plates cover the same rectangular area of roughly 100 mm×70 mm.
Two different types of optical interrogation systems can be used to detect bio-chemical interactions on optical sensors (e.g., surface grating sensors) which are located in multiwell plates. One type of interrogation system is a spectral interrogation system which requires the use of a collimated excitation source that spans or scans through a broad spectral width. The spectral interrogation system also has a receive system which detects changes in the wavelengths associated with the sensor's response to surface chemistry binding. The other type of interrogation system is an angular interrogation system which requires the use of an excitation source (such as a laser) that has a narrow spectral width and spans or scans through a broad range of angles. The angular interrogation system also has a receiver system which detects changes in the angles associated with the sensor's response to surface chemistry binding.
In order to achieve the highest sensitivities and, simultaneously the greatest measurement speed, it is best to measure the fewest number of points possible on the response curve from each sensor and then to fit that curve to determine the response location with sub-sampling (or sub-pixel) accuracy. Typically the minimum number of points required for sampling the response curve with best efficiency is to have on the order of 6 to 10 points lying above the full-width-at-half-maximum (FWHM) of the measured response peak. Fitting of the response may be carried out after filtering the measured response curve, although filtering may not be necessary. Using these fitting methods it is frequently possible to achieve measurement sensitivities on the order of 1/100th of a sampling interval (or pixel). When the requirement for sensitivity approaches this level of sub-sampling resolution, repeatability of the locations sampled on the response curve, as well as the locations interrogated on each sensor, must be ensured to a very high degree. Hence any system which does not require movement or scanning of critical components (e.g. the optical beam, the sensor array, or the receive optics) will have a distinct advantage in sensitivity, repeatability, and speed over systems which do require scanning of critical components.
Scanning methods may be avoided by using highly multiplexed methods, where numerous sets of optical components are dedicated to measuring each of a few individual sensors out of the complete array. However, highly multiplexed systems require many duplicate components, such as lasers, optics, fiber optics, and detectors which can be expensive and complex to construct. In general, it is practical to implement multiplexed optical solutions when the number of sensors to be measured is on the order of tens. However, as the number of sensors in the array approaches 100 or more, these highly multiplexed methods frequently suffer from difficult and high cost of development and construction, poor reliability due to the numerous components, poor uniformity of measured response performance across the array sensors, and difficult serviceability of individual components. Hence measurement systems that use the fewest number of parts and yet enable measurement of every sensor in the array will have a distinct advantage over highly multiplexed systems with regards to manufacturability, reliability, and serviceability.
In another aspect of HTS, single and multi-step assays are often conducted on many different multiwell plates. As an example, for surface index optical sensors, it may be necessary to bind a reactant to a surface, incubate for a period of time, wash the unbound reactant from the sensor, make a reference measurement, introduce a binding-specific specimen of interest, incubate again, wash again, and then measure again to identify a specific binding result. The time scales for each step can be anywhere from seconds to hours. Hence, measurement systems may be required to shuffle many different multiwell plates in and out of the measurement area by either manual or automated plate handling systems. In these situations shifts in the measurement response due to plate replacement need to be measured so that they may be compensated in the measurement results.
Today, systems which use an angular or spectral interrogation approach are developed by utilizing any of the following methods:
(a) Highly Multiplexed Method:
The advantage of this approach is that the critical components can be fixed, thus eliminating the accuracy limitations frequently encountered in a scanning apparatus due to re-positioning errors. However, as described above, when the number of sensors in the array approaches 100 or more, the multiplexed approach frequently suffers from difficult and high cost of construction, poor reliability due to the numerous components, poor uniformity of measured response performance across the array sensors, and difficult serviceability of individual components.
(b) Motion Based Scanning Method:
This method decreases the number of components, cost, and complexity of the instrument by moving critical elements to new positions each time a single or a group of sensors is measured. However, the repeatability of the re-positioning is often the limiting factor in the ability to measure responses with sub-sampling accuracy. In addition, the need to move rapidly to a new specimen location that is a large distance from the previous position (e.g. millimeters) and doing so repeatedly and with high repositioning accuracy (e.g. 100 nm) results in conflicting design requirements for the positioning equipment. These competing requirements necessitate high quality and high cost positioning hardware. Frequently array scanning speed must be sacrificed greatly to ensure an array scanning system's accuracy and repeatability.
(c) Source/Receiver (Angle or Wavelength) Scanning Methods:
These methods either scan the input angle/wavelength or the detected angle/wavelength and measures the response versus time. Such a time division method enables the use of simple and small area optical detectors or allows the mapping of numerous sensors in the array to a smaller area detector. However, when a large dynamic range must be scanned accurately, the time window occupied by the response signal is decreased relative to the entire scan duration, given a fixed (constrained) total scan time. The resulting loss of signal integration time creates an inefficiency that must be compensated for by higher optical power from the source and/or decreased scanning rates. Frequently the repeatability of the scanning limits the sensititivity of the scanning apparatus.
(d) Large Area Components:
This method uses very large area light sources (flood illumination or source arrays) or very large receive components (for example large area CCDs) to simultaneously measure all or a large group of sensors. Unfortunately, large area detector components are very expensive and suffer from slower read out rates when compared to small area detectors. In addition, the use of very large area light sources to illuminate the array can result in power distribution that is severely under-utilized by the sensors in the array. This is particularly true for arrays that contain small area sensors with larger inter-sensor spacing. When using flood illumination, signals associated with multiple sensors or the areas surrounding the sensors often overlap at the detector(s) which causes cross-talk between sensor signals, or interference distortion in the measured response. This interference can limit the accuracy of the measured response of the sensors, particularly when sub-sampling resolution is required.
(e) Array Image Reduction and Mapping Method:
This method maps the responses from locations in the 2-dimensional array of sensors onto a smaller 2-dimensional optical detector. This has the advantage of allowing fewer and smaller area detectors by mapping the different regions of the array to the detector. However, for 2-dimensional array formats, the dynamic range available at the detector for measurement of each sensor's response must be reduced to avoid cross-talk in the detected signals. Also, in this image reduction method, “ghost reflections” may be condensed onto the detector and partially overlap with the desired primary signal. These interference effects then decrease the ability to measure with sub-sampling accuracy.
(f) Array Size Reduction Method:
This method has the advantage of decreasing the total array size that must be measured and with it the dimensions of the corresponding optical hardware and detectors. However, the increase in density of the arrays makes it much more difficult to process and handle the sensors. Array size reduction can require miniaturized components and precision handling. Moreover, this reduction in size does not solve the dynamic range issues associated with approach (e) and can result in increased signal cross-talk of sensor signals at the detector. Furthermore, array size reduction may be contrary to the compatibility requirements associated with standard large area array formats.
It should be noted that combinations of the elements in these six main interrogation approaches (a)-(f) are possible. However, the resulting interrogation system would then have the combined associated advantages, complications and drawbacks described above.
Referring to FIGS. 1A-1C, there are three block diagrams that help illustrate some of the drawbacks associated with the traditional approaches (a)-(f) for interrogating a large two-dimensional array of optical sensors. FIG. 1A shows the problem at hand: large area 2D arrays of optical sensors (S) are measured by using a small area 2D or 1D detector. One approach (b) that is used to try and overcome this problem is shown in FIG. 1B where a row or column of sensors (e.g. S11 . . . SN1 on axis Y) are mapped to the response area of the detector and then critical components are repositioned (scanned) to measure the next column (e.g. S12 . . . SN2) or row of sensors with the same detector area. However, the repeatability of the re-positioning of those critical components is often the limiting factor in the ability of this approach to measure responses with sub-sampled (sub-pixel) accuracy. Another approach (e) that is used to try and overcome this problem is shown in FIG. 1C where the image of the array responses is reduced optically onto the detector. However, presuming a fixed sampling resolution of the detector, this decreases the resolution available to measure each sensor's response relative to the solution of FIG. 1B. This approach of reducing the image also increases the effects of interference from over-lapping of ghost reflections in the system, and possibly sensor cross-talk. Yet another approach (not shown) used to solve this problem is to reduce the image of the array onto the detector and then scan the input or receive angles. Again, it is not desirable to scan critical components, the optical input beam angle, or the receiver angle. Below are listed several patents and publications that describe in greater detail different types of traditional angular interrogation systems:                1) US2003/0007896A1, “Optical Sensor and Optical Process for the Characterization of a Chemical and/or Bio-chemical Substance,” K. Tiefenthaler, Jan. 9, 2003.        2) US2003/0133640 A1, “Waveguide Grid Array and Optical Measurement Arrangement,” K. Tiefenthaler, Jul. 17, 2003.        3) U.S. Pat. No. 5,071,248, “Optical Sensor for Selective Detection of Substances and/or for the Detection of Index of Refraction Changes in Gaseous, Liquid, Solid, and Porous Samples,” K. Tiefenthaler et al., Mar. 28, 1989.        4) U.S. Pat. No. 5,479,260, “Optical Process and Apparatus for Analysis of Substances on Sensor Surfaces,” C. Fattinger, Dec. 26, 1995.        5) U.S. Pat. No. 6,100,991, “Near Normal Incidence Optical Assaying Method and System having Wavelength and Angle Sensitivity,” Challener et al., Aug. 8, 2000.        6) “Grating couplers as chemical sensors: a new optical configuration,” A. Brandenburg and A. Gombert, Sensors and Actuators B, 17 (1993) 35-40.        7) “Real-time Measurement of Nucleic-acids Hybridization Using Evanescent-wave Sensors: Steps Towards the Genosensor,” F. Bier et al., Sensors and Actuators B 38-39, (1997) 78-82.        8) “A multilayer grating-based evanescent wave sensing technique,” W. A. Challener, et al., Sensors and Actuators B 71 (2000) 42-46        9) “Demonstration of Reverse Symmetry Waveguide Sensing in Aqueous Solutions,” R. Horvath et al., App. Phys. Lett., Vol 81, No 12, 16 September 2002, pp 2166-2168        10) U.S. Pat. No. 6,346,376, “Optical Sensor Unit and Procedure for the Ultra-sensitive Detection of Chemical or Biochemical Analytes,” H. Sigrist et al., Feb. 12, 2002.        11) U.S. Pat. No. 6,429,022 B1, “Integrated-optical Sensor and Method for Integrated-optically Sensing a Substance,” R. Kunz et al., Aug. 6, 2002.        12) U.S. Pat. No. 5,313,264, “Optical Biosensor System,” B. Ivarsson et. al., May 17, 1994.        13) US20010026943A1, “SPR Sensor System,” S. Dickopf et al., Oct. 4, 2001.        14) US2002/00001085 A1, “Set-up of Measuring Instruments for the Parallel Readout of SPR Sensors,” S. Dickopf et al., Jan. 3, 2002.The contents of these patents, patent applications and publications are incorporated by reference herein.        
It should be appreciated that several of these patents, patent applications and publications do describe angular interrogation systems that can measure the angular responses from arrays of optical sensors. For instance, traditional angular interrogation systems that re-position the sensors (see ref. 10) or that move or switch critical optical components such as laser sources (see ref. 11) have been detailed. However, the action of switching or moving critical components creates measurement errors that can dominate the level of sensitivity and/or speed that is achievable by the measurement system. Moreover, a traditional angular interrogation system that uses an anamorphic optical receive system for Surface Plasmon Resonance (SPR) measurements is described in ref. 12. However, that system can either a) measure 1-dimensional arrays of sensors, where scanning must be used to address the other dimension of sensors in an array format, or b) image the 2D array of responses from the 2-D sensor array onto the detector area, which limits the resolution available for measuring each sensor's response. Other SPR array angular interrogation systems use array size reduction or image reduction methods for directing responses from two dimensional arrays onto small area detectors (see ref. nos. 13 and 14). However, these types of reduction methods must resort to scanning of the angle (or wavelength) to trace the sensor response functions for the array and as such they have the problematical dynamic range and repeatable scanning issues. As can be seen, it is not easy to scale the systems of these different interrogation approaches (a)-(f) to enable practical high speed and high sensitivity measurements of large arrays of sensors. This need and other needs are satisfied by the optical interrogation systems and methods of the present invention.